Skip to main content

From Molecular Entities to Competent Agents: Viral Infection-Derived Consortia Act as Natural Genetic Engineers

  • Chapter
  • First Online:

Abstract

Endogenous viruses and defectives, transposons, retrotransposons, long terminal repeats, non-long terminal repeats, long interspersed nuclear elements, short interspersed nuclear elements, group I introns, group II introns, phages and plasmids are currently investigated examples that use genomic DNA as their ­preferred live habitat. This means that DNA is not solely a genetic storage medium that serves as an evolutionary protocol, but it is also a species-specific ecological niche. A great variety of such mobile genetic elements have been identified during the last 40 years as obligate inhabitants of all genomes, either prokaryotic or eukaryotic. They infect, insert, delete, some cut and paste, others copy and paste and spread within the genome. They change host genetic identities either by insertion, recombination or the epigenetic (re)regulation of genetic content, and co-evolve with the host and interact in a module-like manner. In this respect they play vital roles in evolutionary and developmental processes. In contrast to accidental point ­mutations, integration at various preferred sites is not a randomly occurring process but is coherent with the genetic content of the host; otherwise, important protein coding regions would be damaged, causing disease or even lethal consequences for the host organism. In contrast to “elements”, “entities” and “systems”, biological agents are capable of identifying sequence-specific loci of genetic text. They are masters of the shared technique of coherently identifying and combining nucleotides according contextual needs. This natural genetic engineering competence is absent in ­inanimate nature, and therefore represents a core capability of life.

“To understand a sentence means to understand a language. To understand a language means to be master of a technique”(Ludwig Wittgenstein)

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Bao W, Kapitonov VV, Jurka J (2010) Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons. Mob DNA 1:3

    Article  PubMed  Google Scholar 

  • Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nat Rev Genet 3:370–380

    Article  PubMed  CAS  Google Scholar 

  • Belousoff MJ, Davidovich C, Zimmerman E et al (2010) Ancient machinery embedded in the contemporary ribosome. Biochem Soc Trans 38:422–427

    Article  PubMed  CAS  Google Scholar 

  • Benelli D, Londei P (2009) Begin at the beginning: evolution of translational initiation. Res Microbiol 160:493–501

    Article  PubMed  CAS  Google Scholar 

  • Bourque G, Leong B, Vega VB et al (2008) Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18:1752–1762

    Article  PubMed  CAS  Google Scholar 

  • Boyer M, Madoui MA, Gimenez G, La Scola B et al (2011) Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4th domain of life including giant viruses. PLoS One 5(12):e15530

    Article  Google Scholar 

  • Bredy TW, Lin Q, Wei W, Baker Andresen D et al (2011) Mirco RNA regulation of neural plasticity and memory. Neurobiol Learn Mem 96:89–94

    Article  PubMed  CAS  Google Scholar 

  • Brüssow H (2007) The quest for food a natural history of eating. Springer, New York

    Google Scholar 

  • Delelis O, Carayon K, Saib A, Deprez E et al (2008) Integrase and integration: biochemical activities of HIV-I integrase. Retrovirol 5:114

    Article  Google Scholar 

  • Dixon RJ, Eperon IA, Samani NJ (2007) Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. Bioinformatics 23:150–155

    Article  PubMed  CAS  Google Scholar 

  • Domingo E (2011) Paradoxical interplay of viral and cellular functions. Viruses 3:272–277

    Article  PubMed  CAS  Google Scholar 

  • Eickbush TH (2002) Repair by retrotransposition. Nat Genet 31:126–127

    Article  PubMed  CAS  Google Scholar 

  • Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134:221–234

    Article  PubMed  CAS  Google Scholar 

  • Eickbush TH, Malik HS (2002) Evolution of retrotransposons. In: Craig N, Craigie R, Gellert M, Lambowitz A (eds) Mobile DNA II. American Society of Microbiology Press, Washington, DC, pp 1111–1144

    Google Scholar 

  • Felice B, Cattoglio C, Cittaro D, Testa A et al (2009) Transcription factor binding sites are genetic determinants of retroviral integration in the human genome. PLoS One 4:e4571

    Article  PubMed  Google Scholar 

  • Feschotte C (2008) Transposable elements and the evolution of regulatory networks. Nat Rev Genet 9:397–405

    Article  PubMed  CAS  Google Scholar 

  • Forterre P (2005) The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells. Biochimie 87:793–803

    Article  PubMed  CAS  Google Scholar 

  • Forterre P (2006) The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 117:5–16

    Article  PubMed  CAS  Google Scholar 

  • Forterre P (2011) A new fusion hypothesis for the origin of Eukarya: better than previous ones, but probably also wrong. Res Microbiol 162:77–91

    Article  PubMed  CAS  Google Scholar 

  • Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722–732

    Article  PubMed  CAS  Google Scholar 

  • Gao X, Havecker ER, Baranov PV et al (2003) Translational recoding signals between gag and pol in diverse LTR retrotransposons. RNA 9:1422–1430

    Article  PubMed  CAS  Google Scholar 

  • Geuking MB, Weber J, Dewannieux M, Gorelik ME et al (2009) Recombination of retrotransposon and exogenous RNA virus results in nonretroviral cDNA integration. Science 323:393–396

    Article  PubMed  CAS  Google Scholar 

  • Gimenez J, Montgiraud C, Oriol G et al (2009) Comparative methylation of ERVWE1/syncytin-1 and other human endogenous retrovirus LTRs in placenta tissues. DNA Res 16:195–211

    Article  PubMed  CAS  Google Scholar 

  • Goodier JL, Kazazian HH (2008) Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135:23–35

    Article  PubMed  CAS  Google Scholar 

  • Hambly E, Suttle CA (2005) The virosphere, diversity and genetic exchange within phage ­communities. Curr Opin Microbiol 8:444–450

    Article  PubMed  CAS  Google Scholar 

  • Holmes EC (2011) What does virus evolution tell us about virus origins? J Virol 85:5247–5251

    Article  PubMed  CAS  Google Scholar 

  • Horie M, Tomonaga K (2011) Non-retroviral fossils in Vertebrate genomes. Viruses 3:1836–1848

    Article  PubMed  CAS  Google Scholar 

  • Hua-Van A, Le Rouzic A, Boutin TS, Filee J et al (2011) The struggle for life of the genome’s selfish architects. Biol Direct 6:19

    Article  PubMed  Google Scholar 

  • Huda A, Jordan IK (2009) Epigenetic regulation of mammalian genomes by transposable ­elements. Ann N Y Acad Sci 1178:276–284

    Article  PubMed  CAS  Google Scholar 

  • Huda A, Mariño-Ramírez L, Jordan IK (2010) Epigenetic histone modifications of human ­transposable elements: genome defense versus exaptation. Mob DNA 25:2

    Article  Google Scholar 

  • Hunter P (2008) The great leap forward major evolutionary jumps might be caused by changes in gene regulation rather than the emergence of new genes. EMBO Rep 9:608–611

    Article  PubMed  CAS  Google Scholar 

  • Jurka J, Kapitonov VV, Kohany O, Jurka MV (2007) Repetitive sequences in complex genomes: structure and evolution. Annu Rev Genomics Hum Genet 8:241–259

    Article  PubMed  CAS  Google Scholar 

  • Kapitonov VV, Jurka J (2008) A universal classification of eukaryotic transposable elements implemented in repbase. Nat Rev Genet 9:411–412

    Article  PubMed  Google Scholar 

  • Kim SY, Pritvjard JK (2007) Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet 3:e147

    Article  Google Scholar 

  • Klenerman P, Hengartner H, Zinkernagel RM (1997) A non-retroviral RNA virus persists in DNA form. Nature 390:298–301

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV (2009) On the origin of cells and viruses: primordial virus world scenario. Ann N Y Acad Sci 1178:47–64

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV, Senkevich TG, Dolja VV (2006) The ancient virus world and evolution of cells. Biol Direct 1:29

    Article  PubMed  Google Scholar 

  • Lambowitz AK, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35

    Article  PubMed  CAS  Google Scholar 

  • Le Rouzic A, Dupas S, Capy P (2007) Genome ecosystem and transposable elements species. Gene 390:214–220

    Article  PubMed  Google Scholar 

  • Levin HL, Moran JV (2011) Dynamic interactions between transposable elements and their hosts. Nat Rev Genet 12:615–627

    Article  PubMed  CAS  Google Scholar 

  • Lolle SJ, Victor JL, Young JM et al (2002) Genome-wide non-mendelian inheritance of extragenomic information in Arabidopsis. Nature 434:505–509

    Article  Google Scholar 

  • Mahajan VS, Drake A, Chen J (2008) Virus-specific host miRNAs: antiviral defenses or promotors of persistent infection? Trends Immunol 30:1–7

    Article  PubMed  Google Scholar 

  • Maizels N, Weiner AM, Yue D et al (1999) New evidence for the genomic tag hypothesis: archaeal CCA-adding enzymes and tRNA substrates. Biol Bull 196:331–334

    Article  PubMed  CAS  Google Scholar 

  • Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668

    Article  PubMed  CAS  Google Scholar 

  • Marraffini A, Sontheimer EJ (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nature 11:181–190

    CAS  Google Scholar 

  • Moore PB, Steitz TA (2006) The roles of RNA in the synthesis of protein. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world, 3rd edn. Cold Spring Harbor Laboratory Press, New York, pp 257–285

    Google Scholar 

  • O’Donnell KA, Burns KH (2010) Mobilizing diversity: transposable element insertions in genetic variation and disease. Mob DNA 1:21

    Article  PubMed  Google Scholar 

  • Pearson H (2005) Cress overturns textbook genetics. Nature 434:351–360

    Article  Google Scholar 

  • Phizicky EM (2005) Have tRNA, will travel. Proc Natl Acad Sci USA 102:11127–11128

    Article  PubMed  CAS  Google Scholar 

  • Randau L, Söll D (2008) Transfer RNA genes in pieces. EMBO Rep 9:623–628

    Article  PubMed  CAS  Google Scholar 

  • Roossinck MJ (2011) The good viruses: viral mutualistic symbiosis. Nat Rev Microbiol 9:99–108

    Article  PubMed  CAS  Google Scholar 

  • Schmitz J, Brosius J (2011) Exonization of transposed elements: a challenge and opportunity for evolution. Biochimie 93:1928–1934

    Article  PubMed  CAS  Google Scholar 

  • Shapiro JA (2011) Evolution: a view from the 21st century. Financial Times Prentice Hall, New York

    Google Scholar 

  • Shapiro JA, Sternberg R (2005) Why repetitive DNA is essential to genome function. Biol Rev 80:1–24

    Article  Google Scholar 

  • Simon-Loriere E, Holmes EC (2011) Why do RNA viruses recombine. Nat Rev Microbiol 9:617–626

    Article  PubMed  CAS  Google Scholar 

  • Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272–285

    Article  PubMed  CAS  Google Scholar 

  • Smalheiser NR, Torvik VI (2006) Alu elements within human mRNAs are probable microRNA targets. Trends Genet 22:532–536

    Article  PubMed  CAS  Google Scholar 

  • Sternberg R, Shapiro JA (2005) How repeated retroelements format genome function. Cytogenet Genome Res 110:108–116

    Article  Google Scholar 

  • Stoddard B, Belfort M (2010) Social networking between mobile introns and their host genes. Mol Microbiol 78:1–4

    PubMed  CAS  Google Scholar 

  • Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5:801–812

    Article  PubMed  CAS  Google Scholar 

  • Venner S, Feschotte C, Biemont C (2009) Transposable elements dynamics: towards a community ecology of the genome. Trends Genet 25:317–323

    Article  PubMed  CAS  Google Scholar 

  • Villarreal LP (2005) Viruses and the evolution of life. American Society for Microbiology Press, Washington, DC

    Google Scholar 

  • Villarreal LP (2007) Virus-host symbiosis mediated by persistence. Symbiosis 44:1–9

    CAS  Google Scholar 

  • Villarreal LP (2009a) The source of self: Genetic parasites and the origin of adaptive immunity. Ann NY Acad Sci 1178:194–232

    Google Scholar 

  • Villarreal LP (2009b) Origin of group identity: Viruses, addiction and cooperation. Springer, New York

    Google Scholar 

  • Villarreal LP (2011) Viral ancestors of antiviral systems. Viruses 3:1933–1958

    Article  PubMed  CAS  Google Scholar 

  • Villarreal LP (2012) Viruses and host evolution: virus-mediated self identity. In: Lopez-Larrea C (ed) Self and non-self. LandesBioScience/Springer, Austin

    Google Scholar 

  • Villarreal LP, Witzany G (2010) Viruses are essential agents within the roots and stem of the tree of life. J Theor Biol 262:698–710

    Article  PubMed  Google Scholar 

  • Volff JN (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 28:913–922

    Article  PubMed  CAS  Google Scholar 

  • Weber MJ (2006) Mammalian small nucleolar RNAs Are mobile genetic elements. PLoS Genet 2:1984–1997

    Article  CAS  Google Scholar 

  • Wegrzyn G, Wegrzyn A (2008) Is tRNA only a translation factor or also a regulator of other ­processes? J Appl Genet 49:115–122

    Article  PubMed  Google Scholar 

  • Wessler S (2006) Eukaryotic transposable elements: teaching old genomes new tricks. In: Caporale L (ed) The implicit genome. Oxford University Press, New York, pp 139–162

    Google Scholar 

  • Witzany G (2008) The viral origins of telomeres, telomerases and their important role in eukaryogenesis and genome maintenance. Biosem 2:191–206

    Article  Google Scholar 

  • Witzany G (ed) (2009a) Natural genetic engineering and natural genome editing. Wiley Blackwell, Boston

    Google Scholar 

  • Witzany G (2009b) Non-coding RNAs: persistent viral agents as modular tools for cellular needs. Ann N Y Acad Sci 1178:244–267

    Article  PubMed  CAS  Google Scholar 

  • Witzany G (2010) Biocommunication and natural genome editing. Springer, Dordrecht

    Book  Google Scholar 

  • Witzany G (2011a) The agents of natural genome editing. J Mol Cell Biol 3:181–189

    Article  PubMed  CAS  Google Scholar 

  • Witzany G (ed) (2011b) Biocommunication in soil microorganisms. Springer, Heidelberg

    Google Scholar 

  • Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–1530

    Article  PubMed  CAS  Google Scholar 

  • Xiong Y, Eickbush TH (1988) Similarity of reverse transcriptase-like sequences of viruses, transposable elements and mitochondrial introns. Mol Biol Evol 5:675–690

    PubMed  CAS  Google Scholar 

  • Xiong Y, Steitz TA (2004) Mechanism of transfer RNA maturation by CCA-adding enzyme ­without using an oligonucleotide template. Nature 430:640–645

    Article  PubMed  CAS  Google Scholar 

  • Zhsang Z, Saier MH (2009) A mechanism of transposon-mediated directed mutation. Mol Microbiol 74:29–43

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Günther Witzany .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Witzany, G. (2012). From Molecular Entities to Competent Agents: Viral Infection-Derived Consortia Act as Natural Genetic Engineers. In: Witzany, G. (eds) Viruses: Essential Agents of Life. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4899-6_20

Download citation

Publish with us

Policies and ethics